AI agents call pdb_get_nonpolymer_entity_instance to retrieve information from OrigeneMCP without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
The 'get_' prefix and PDB context indicate this tool retrieves information about non-polymer entities (ligands, ions, water molecules) in protein structures without modifying data. Sibling tools on OrigeneMCP are uniformly information-retrieval functions. No evidence of write, execute, delete, or financial operations. Severity is low because retrieving structural data carries minimal risk of misuse by an AI agent.
From the tool's definition Tool name 'pdb_get_nonpolymer_entity_instance' uses the 'get' verb, indicating data retrieval. The PDB (Protein Data Bank) context suggests querying structural biology data.
Documented attack patterns abuse exactly the kind of access pdb_get_nonpolymer_entity_instance gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and OrigeneMCP, and nothing reaches the server without passing your rules. This is the rule we recommend for pdb_get_nonpolymer_entity_instance:
{
"version": "1",
"default": "deny",
"tools": {
"pdb_get_nonpolymer_entity_instance": {}
}
}pdb_get_nonpolymer_entity_instance is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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pdb_get_nonpolymer_entity_instance. It is categorised as a Read tool in the OrigeneMCP MCP Server, which means it retrieves data without modifying state.
Register the Origene MCP server in PolicyLayer and add a rule for pdb_get_nonpolymer_entity_instance: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches OrigeneMCP. Nothing to install.
pdb_get_nonpolymer_entity_instance is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the pdb_get_nonpolymer_entity_instance rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for pdb_get_nonpolymer_entity_instance. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
pdb_get_nonpolymer_entity_instance is provided by the Origene MCP server (gentel-lab/origenemcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from OrigeneMCP, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
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439 OrigeneMCP tools catalogued and risk-classified — across an index of 43,000+ MCP servers.